{
  "_id": "6a547f12ff0138dec5d6432b",
  "Package": "MLP",
  "Maintainer": "Tobias Verbeke <tobias.verbeke@openanalytics.eu>",
  "License": "GPL-3",
  "Title": "Mean Log P Analysis",
  "Type": "Package",
  "Authors@R": "c(\nperson(given = \"Nandini\", family = \"Raghavan\", role = \"aut\"),\nperson(given = \"Tobias\", family = \"Verbeke\", role = \"aut\", email = \"tobias.verbeke@openanalytics.eu\"),\nperson(given = \"An\", family = \"De Bondt\", role = \"aut\"),\nperson(given = \"Javier\", family = \"Cabrera\", role = \"ctb\"),\nperson(given = \"Dhammika\", family = \"Amaratunga\", role = \"ctb\"),\nperson(given = \"Tine\", family = \"Casneuf\", role = \"ctb\"),\nperson(given = \"Willem\", family = \"Ligtenberg\", role = \"ctb\"),\nperson(given = \"Laure\", family = \"Cougnaud\", role = \"cre\", email = \"laure.cougnaud@openanalytics.eu\"),\nperson(given = \"Katarzyna\", family = \"Gorczak\", role = \"ctb\", email = \"katarzyna.gorczak@openanalytics.eu\")\n)",
  "Description": "Pathway analysis based on p-values associated to genes\nfrom a genes expression analysis of interest. Utility functions\nenable to extract pathways from the Gene Ontology Biological\nProcess (GOBP), Molecular Function (GOMF) and Cellular\nComponent (GOCC), Kyoto Encyclopedia of Genes of Genomes (KEGG)\nand Reactome databases. Methodology, and helper functions to\ndisplay the results as a table, barplot of pathway\nsignificance, Gene Ontology graph and pathway significance are\navailable.",
  "Version": "1.61.0",
  "biocViews": "Genetics, GeneExpression, Pathways, Reactome, KEGG, GO",
  "Date": "2025-04-22",
  "Collate": "'addGeneSetDescription.R' 'getGeneSets.R' 'mlpBarplot.R'\n'MLP.R' 'plotGeneSetSignificance.R' 'plotGOgraph.R'\n'plot.MLP.R' 'plotQuantileCurves.R' 'utils.R'",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "libpng-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:35:00 UTC",
  "RemoteUrl": "https://github.com/bioc/MLP",
  "RemoteRef": "HEAD",
  "RemoteSha": "14fdc6f434ab13596bf5b680ef028b636770edb3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-13 05:46:45 UTC",
    "User": "root"
  },
  "Author": "Nandini Raghavan [aut],\nTobias Verbeke [aut],\nAn De Bondt [aut],\nJavier Cabrera [ctb],\nDhammika Amaratunga [ctb],\nTine Casneuf [ctb],\nWillem Ligtenberg [ctb],\nLaure Cougnaud [cre],\nKatarzyna Gorczak [ctb]",
  "_user": "bioc",
  "_type": "src",
  "_file": "MLP_1.61.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/ef2e95c5a5f18f28eba9a684ff37e3f1d41306378cab9e06266a4f4b03cbbd60",
  "_filesize": 4446097,
  "_sha256": "ef2e95c5a5f18f28eba9a684ff37e3f1d41306378cab9e06266a4f4b03cbbd60",
  "_expires": "2026-10-21T06:00:48.000Z",
  "_created": "2026-07-13T05:46:45.000Z",
  "_published": "2026-07-13T06:00:50.689Z",
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 10
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29226884448",
  "_status": "success",
  "_upstream": "https://github.com/bioc/MLP",
  "_commit": {
    "id": "14fdc6f434ab13596bf5b680ef028b636770edb3",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379700
  },
  "_maintainer": {
    "name": "Tobias Verbeke",
    "email": "tobias.verbeke@openanalytics.eu",
    "login": "tverbeke",
    "description": "",
    "uuid": 5047312
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 86743594108,
      "time": 338,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8270246815"
    },
    {
      "job": 86743594156,
      "time": 788,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8270357587"
    },
    {
      "job": 86743594142,
      "time": 797,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8270359777"
    },
    {
      "job": 86743594128,
      "time": 517,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "8270290443"
    },
    {
      "job": 86743594117,
      "time": 646,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8270322175"
    },
    {
      "job": 86742790973,
      "time": 389,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8270162513"
    },
    {
      "job": 86743594130,
      "time": 302,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8270237205"
    },
    {
      "job": 86743594141,
      "time": 643,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8270322314"
    },
    {
      "job": 86743594132,
      "time": 669,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "8270328746"
    },
    {
      "job": 86743594136,
      "time": 666,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8270328813"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "gplots",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "GO.db",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Mm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Rn.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Cf.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Mmu.eg.db",
      "role": "Suggests"
    },
    {
      "package": "KEGGREST",
      "role": "Suggests"
    },
    {
      "package": "annotate",
      "role": "Suggests"
    },
    {
      "package": "Rgraphviz",
      "role": "Suggests"
    },
    {
      "package": "GOstats",
      "role": "Suggests"
    },
    {
      "package": "graph",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "mouse4302.db",
      "role": "Suggests"
    },
    {
      "package": "reactome.db",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.61.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.60.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "genetics",
    "geneexpression",
    "pathways",
    "reactome",
    "kegg",
    "go"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 446,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 592,
    "source": "https://www.bioconductor.org/packages/stats/bioc/MLP"
  },
  "_mentions": 37,
  "_searchresults": 11,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MLP.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addGeneSetDescription",
    "getGeneSets",
    "MLP",
    "mlpBarplot",
    "plotGeneSetSignificance",
    "plotGOgraph"
  ],
  "_help": [
    {
      "page": "addGeneSetDescription",
      "title": "Utility function which adds the biological description of the gene sets as a column to the return value of the MLP function (data frame)",
      "topics": [
        "addGeneSetDescription"
      ]
    },
    {
      "page": "getGeneSets",
      "title": "Prepare Pathway Data for the MLP Function",
      "topics": [
        "getGeneSets"
      ]
    },
    {
      "page": "MLP",
      "title": "This function calculates p-values for each gene set based on row permutations of the gene p values or column permutations of the expression matrix; the p values can be obtained either as individual gene set p values or p values based on smoothing across gene sets of similar size.",
      "topics": [
        "MLP"
      ]
    },
    {
      "page": "mlpBarplot",
      "title": "Draw a Barplot for MLP Results",
      "topics": [
        "mlpBarplot"
      ]
    },
    {
      "page": "plot.MLP",
      "title": "Plot the Results of an MLP Run",
      "topics": [
        "plot.MLP"
      ]
    },
    {
      "page": "plotGeneSetSignificance",
      "title": "Plot the Significance for the Genes of a Given Gene Set",
      "topics": [
        "plotGeneSetSignificance"
      ]
    },
    {
      "page": "plotGOgraph",
      "title": "Graphical Representation of GO Based MLP Results",
      "topics": [
        "plotGOgraph"
      ]
    }
  ],
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "caTools",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "fastmap",
    "generics",
    "glue",
    "gplots",
    "gtools",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "lifecycle",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "png",
    "R6",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "sys",
    "vctrs",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "UsingMLP.Rnw",
      "filename": "UsingMLP.pdf",
      "title": "UsingMLP",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "Example Use",
        "References"
      ],
      "created": "2013-11-01 20:15:57",
      "modified": "2021-11-19 14:37:31",
      "commits": 7
    }
  ],
  "_score": 4.819543935541869,
  "_indexed": true,
  "_nocasepkg": "mlp",
  "_universes": [
    "bioc",
    "tverbeke"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.61.0",
      "date": "2026-07-13T05:53:20.000Z",
      "distro": "resolute",
      "commit": "14fdc6f434ab13596bf5b680ef028b636770edb3",
      "fileid": "https://r2.ropensci.org/21185ff36c4ee707c2e2bd940ed65c040e25d621257bf07a1c084764df65e2a5",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29226884448"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.61.0",
      "date": "2026-07-13T05:53:19.000Z",
      "distro": "resolute",
      "commit": "14fdc6f434ab13596bf5b680ef028b636770edb3",
      "fileid": "https://r2.ropensci.org/43b66a44accbf0ab4e229c5c6cb1395a658953a4d93293eba04f5f261535f824",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29226884448"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.61.0",
      "date": "2026-07-13T05:49:37.000Z",
      "commit": "14fdc6f434ab13596bf5b680ef028b636770edb3",
      "fileid": "https://r2.ropensci.org/08f18669f7cab139d0708934cfc6c6fd9cae58bfac620e977be636ed7184a505",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29226884448"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.61.0",
      "date": "2026-07-13T05:49:41.000Z",
      "commit": "14fdc6f434ab13596bf5b680ef028b636770edb3",
      "fileid": "https://r2.ropensci.org/6a629cab08cff84f01937975ab2ea0e906cd62248e42aae6b416dfb8b772eabc",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29226884448"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.61.0",
      "date": "2026-07-13T05:52:04.000Z",
      "commit": "14fdc6f434ab13596bf5b680ef028b636770edb3",
      "fileid": "https://r2.ropensci.org/e4ca169e9bcec588da289cb38ec3301c25a69d075e01d124a375caa31239f4f3",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29226884448"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.61.0",
      "date": "2026-07-13T05:50:28.000Z",
      "commit": "14fdc6f434ab13596bf5b680ef028b636770edb3",
      "fileid": "https://r2.ropensci.org/8af54c6efd66fa5cc9dadc96737d2946d86de6500809cc1c93be35fc654e2eb3",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29226884448"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.61.0",
      "date": "2026-07-13T05:50:28.000Z",
      "commit": "14fdc6f434ab13596bf5b680ef028b636770edb3",
      "fileid": "https://r2.ropensci.org/deeaccdf01b5aa3bf7b5aa08d1b09003c544a7d391a3c0e909f40d01e915ca09",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29226884448"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.61.0",
      "date": "2026-07-13T05:51:06.000Z",
      "commit": "14fdc6f434ab13596bf5b680ef028b636770edb3",
      "fileid": "https://r2.ropensci.org/7410a51e90ba3d1042498f04ffb8ef437ae8b982eb77324a51be85819f2ab7bd",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29226884448"
    }
  ]
}